guacamole

Guacamole is a framework for variant calling, i.e. identifying DNA mutations from Next Generation Sequencing data. It currently includes a toy germline (non-cancer) variant caller as well as a somatic variant caller for finding cancer mutations. Most development effort has gone into the somatic caller so far.

The emphasis is on a readable codebase that can be readily understood and adapted for experimentation.

Guacamole is written in Scala using the Apache Spark engine for distributed processing. It can run on a single computer or on a Hadoop cluster.

Guacamole supports reading aligned reads as:

• BAM or SAM files
• Parquet files of bdg-formats AlignmentRecords

It can write the called genotypes as:

• VCF files
• Parquet files of bdg-formats Genotypes.

Guacamole uses ideas and some functionality from ADAM. It also takes inspiration from the Avocado project.

For hacking Guacamole, see our code docs.

Running Guacamole on a Single Node

Guacamole requires Apache Maven.

Build:

mvn package

This will build a guacamole JAR file in the target directory. A script is included to run it:

scripts/guacamole germline-threshold \
	-reads src/test/resources/chrM.sorted.bam \
	-out /tmp/result.vcf

This creates a directory called /tmp/result.vcf. The actual VCF file is in /tmp/result.vcf/part-r-00000. You'll always get one part file in the output directory.

Try

scripts/guacamole -h

for a list of implemented variant callers, or

scripts/guacamole <caller> -h

for help on a particular variant caller.

Running Guacamole on a Hadoop Cluster

See Guacamole's pom.xml file for the versions of Hadoop and Spark that Guacamole expects to find on your cluster.

Here is an example command to get started using Guacamole in Spark's yarn cluster mode. You'll probably have to modify it for your environment.

spark-submit \
	--master yarn \
	--deploy-mode cluster \
	--driver-java-options -Dlog4j.configuration=/path/to/guacamole/scripts/log4j.properties \
	--executor-memory 4g \
	--driver-memory 10g \
	--num-executors 1000 \
	--executor-cores 1 \
	--class org.hammerlab.guacamole.Guacamole \
	--verbose \
	/path/to/target/guacamole-0.0.1.jar \
	germline-threshold \
        -reads hdfs:///path/to/reads.bam \
        -out hdfs:///path/to/result.vcf \
	-spark_master yarn-cluster

Is this ready for production use?

Not currently. Everything here is experimental. Please use a standard tool if you need accurate variant calls.

License

Guacamole is released under an Apache 2.0 license.

YourKit is kindly supporting this open source project with its full-featured Java Profiler. YourKit, LLC is the creator of innovative and intelligent tools for profiling Java and .NET applications.